Genomic analysis of distinct bleaching tolerances among cryptic coral species

2021 ◽  
Vol 288 (1960) ◽  
Author(s):  
Noah H. Rose ◽  
Rachael A. Bay ◽  
Megan K. Morikawa ◽  
Luke Thomas ◽  
Elizabeth A. Sheets ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Coral Species ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Species Traits ◽  
American Samoa ◽  
Bleaching Event ◽  
Nucleotide Polymorphisms ◽  
Full Genome Sequencing ◽  
Resistant Species

Reef-building coral species are experiencing an unprecedented decline owing to increasing frequency and intensity of marine heatwaves and associated bleaching-induced mortality. Closely related species from the Acropora hyacinthus species complex differ in heat tolerance and in their association with heat-tolerant symbionts. We used low-coverage full genome sequencing of 114 colonies monitored across the 2015 bleaching event in American Samoa to determine the genetic differences among four cryptic species (termed HA, HC, HD and HE) that have diverged in these species traits. Cryptic species differed strongly at thousands of single nucleotide polymorphisms across the genome which are enriched for amino acid changes in the bleaching-resistant species HE. In addition, HE also showed two particularly divergent regions with strong signals of differentiation. One approximately 220 kb locus, HES1, contained the majority of fixed differences in HE. A second locus, HES2, was fixed in HE but polymorphic in the other cryptic species. Surprisingly, non-HE individuals with HE-like haplotypes at HES2 were more likely to bleach. At both loci, HE showed particular sequence similarity to a congener, Acropora millepora . Overall, resilience to bleaching during the third global bleaching event was strongly structured by host cryptic species, buoyed by differences in symbiont associations between these species.

scholarly journals High Frequency of a Novel Filamentous Phage, VCYϕ, within an Environmental Vibrio cholerae Population

2011 ◽  
Vol 78 (1) ◽  
pp. 28-33 ◽  
Author(s):  
Hong Xue ◽  
Yan Xu ◽  
Yan Boucher ◽  
Martin F. Polz
Keyword(s):  
Vibrio Cholerae ◽  
Sequence Similarity ◽  
Host Population ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Filamentous Phage ◽  
Nucleotide Polymorphisms ◽  
Environmental Biology ◽  
Content Type ◽  
Filamentous Phages

ABSTRACTEnvironmentalVibrio choleraestrains isolated from a coastal brackish pond (Oyster Pond, Woods Hole, MA) carried a novel filamentous phage, VCYϕ, which can exist as a host genome integrative form (IF) and a plasmid-like replicative form (RF). Outside the cell, the phage displays a morphology typical ofInovirus, with filamentous particles ∼1.8 μm in length and 7 nm in width. Four independent RF isolates had identical genomes, except for 8 single nucleotide polymorphisms clustered in two regions. The overall genome size is 7,103 bp with 11 putative open reading frames organized into three functional modules (replication, structure and assembly, and regulation). VCYϕ shares sequence similarity with other filamentous phages (including cholera disease-associated CTX) in a highly mosaic manner, indicating evolution by horizontal gene transfer and recombination. VCYϕ integrates in the vicinity of the putative translation initiation factor Sui1 in chromosome II ofV. cholerae. A screen of 531 closely related host isolates showed that ∼40% harbored phages, with 27% and 13% carrying the IF and RF, respectively. The relative frequencies of the RF and IF differed among strains isolated from the pond or lagoon of Oyster Pond, suggesting that the host habitat influences intracellular phage biology. The overall high prevalence within the host population shows that filamentous phages can be an important component of the environmental biology ofV. cholerae.

scholarly journals Seascape genomics reveals candidate molecular targets of heat stress adaptation in three coral species

2020 ◽  
Author(s):  
Oliver Selmoni ◽  
Gaël Lecellier ◽  
Hélène Magalon ◽  
Laurent Vigliola ◽  
Francesca Benzoni ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Mechanisms ◽  
Coral Species ◽  
New Caledonia ◽  
Heat Waves ◽  
Molecular Targets ◽  
Remote Sensing Data ◽  
Stress Adaptation ◽  
Nucleotide Polymorphisms ◽  
Apoptotic Pathways

AbstractAnomalous heat waves are causing a major decline of hard corals around the world and threatening the persistence of coral reefs. There are, however, reefs that had been exposed to recurrent thermal stress over the years and whose corals appeared tolerant against heat. One of the mechanisms that could explain this phenomenon is local adaptation, but the underlying molecular mechanisms are poorly known.In this work, we applied a seascape genomics approach to study heat stress adaptation in three coral species of New Caledonia (southwestern Pacific) and to uncover molecular actors potentially involved. We used remote sensing data to characterize the environmental trends across the reef system, and sampled corals living at the most contrasted sites. These samples underwent next generation sequencing to reveal single-nucleotide-polymorphisms (SNPs) of which frequencies associated with heat stress gradients. As these SNPs might underpin an adaptive role, we characterized the functional roles of the genes located in their genomic neighborhood.In each of the studied species, we found heat stress associated SNPs notably located in proximity of genes coding for well-established actors of the cellular responses against heat. Among these, we can mention proteins involved in DNA damage-repair, protein folding, oxidative stress homeostasis, inflammatory and apoptotic pathways. In some cases, the same putative molecular targets of heat stress adaptation recurred among species.Together, these results underscore the relevance and the power of the seascape genomics approach for the discovery of adaptive traits that could allow corals to persist across wider thermal ranges.

scholarly journals Genomic analysis of family data reveals additional genetic effects on intelligence and personality

2017 ◽  
Author(s):  
W. David Hill ◽  
Ruben C. Arslan ◽  
Charley Xia ◽  
Michelle Luciano ◽  
Carmen Amador ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Molecular Genetic ◽  
Copy Number Variants ◽  
Twin Studies ◽  
Genomic Analysis ◽  
Heritability Estimate ◽  
Genetic Effects ◽  
Genetic Differences ◽  
Substantial Contribution ◽  
Nucleotide Polymorphisms

AbstractPedigree-based analyses of intelligence have reported that genetic differences account for 50-80% of the phenotypic variation. For personality traits these effects are smaller, with 34-48% of the variance being explained by genetic differences. However, molecular genetic studies using unrelated individuals typically report a heritability estimate of around 30% for intelligence and between 0% and 15% for personality variables. Pedigree-based estimates and molecular genetic estimates may differ because current genotyping platforms are poor at tagging causal variants, variants with low minor allele frequency, copy number variants, and structural variants. Using ∼20 000 individuals in the Generation Scotland family cohort genotyped for ∼700 000 single nucleotide polymorphisms (SNPs), we exploit the high levels of linkage disequilibrium (LD) found in members of the same family to quantify the total effect of genetic variants that are not tagged in GWASs of unrelated individuals. In our models, genetic variants in low LD with genotyped SNPs explain over half of the genetic variance in intelligence, education, and neuroticism. By capturing these additional genetic effects our models closely approximate the heritability estimates from twin studies for intelligence and education, but not for neuroticism and extraversion. We then replicated our finding using imputed molecular genetic data from unrelated individuals to show that ∼50% of differences in intelligence, and ∼40% of the differences in education, can be explained by genetic effects when a larger number of rare SNPs are included. From an evolutionary genetic perspective, a substantial contribution of rare genetic variants to individual differences in intelligence and education is consistent with mutation-selection balance.

scholarly journals Strain-Specific Genotyping of Bifidobacterium animalis subsp. lactis by Using Single-Nucleotide Polymorphisms, Insertions, and Deletions

2009 ◽  
Vol 75 (23) ◽  
pp. 7501-7508 ◽  
Author(s):  
Elizabeth P. Briczinski ◽  
Joseph R. Loquasto ◽  
Rodolphe Barrangou ◽  
Edward G. Dudley ◽  
Anastasia M. Roberts ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Sequence Similarity ◽  
Nucleotide Polymorphisms ◽  
Strain Specificity ◽  
Typing Method ◽  
Single Nucleotide ◽  
Bifidobacterium Animalis ◽  
Molecular Approaches ◽  
Commercial Applications ◽  
High Level

ABSTRACT Several probiotic strains of Bifidobacterium animalis subsp. lactis are widely supplemented into food products and dietary supplements due to their documented health benefits and ability to survive within the mammalian gastrointestinal tract and acidified dairy products. The strain specificity of these characteristics demands techniques with high discriminatory power to differentiate among strains. However, to date, molecular approaches, such as pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR, have been ineffective at achieving strain separation due to the monomorphic nature of this subspecies. Previously, sequencing and comparison of two B. animalis subsp. lactis genomes (DSMZ 10140 and Bl-04) confirmed this high level of sequence similarity, identifying only 47 single-nucleotide polymorphisms (SNPs) and four insertions and/or deletions (INDELs) between them. In this study, we hypothesized that a sequence-based typing method targeting these loci would permit greater discrimination between strains than previously attempted methods. Sequencing 50 of these loci in 24 strains of B. animalis subsp. lactis revealed that a combination of nine SNPs/INDELs could be used to differentiate strains into 14 distinct genotypic groups. In addition, the presence of a nonsynonymous SNP within the gene encoding a putative glucose uptake protein was found to correlate with the ability of certain strains to transport glucose and to grow rapidly in a medium containing glucose as the sole carbon source. The method reported here can be used in clinical, regulatory, and commercial applications requiring identification of B. animalis subsp. lactis at the strain level.

scholarly journals Identification of Allelic Variation in Drought Responsive Dehydrin Gene Based on Sequence Similarity in Chickpea (Cicer arietinum L.)

2020 ◽  
Vol 11 ◽  
Author(s):  
Tapan Kumar ◽  
Neha Tiwari ◽  
Chellapilla Bharadwaj ◽  
Ashutosh Sarker ◽  
Sneha Priya Reddy Pappula ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Drought Tolerance ◽  
Cicer Arietinum ◽  
Allelic Variation ◽  
Sequence Similarity ◽  
Nucleotide Polymorphisms ◽  
Residual Moisture ◽  
Single Nucleotide ◽  
The World ◽  
Dehydrin Gene

Chickpea (Cicer arietinum L.) is an economically important food legume grown in arid and semi-arid regions of the world. Chickpea is cultivated mainly in the rainfed, residual moisture, and restricted irrigation condition. The crop is always prone to drought stress which is resulting in flower drop, unfilled pods, and is a major yield reducer in many parts of the world. The present study elucidates the association between candidate gene and morpho-physiological traits for the screening of drought tolerance in chickpea. Abiotic stress-responsive gene Dehydrin (DHN) was identified in some of the chickpea genotypes based on the sequence similarity approach to play a major role in drought tolerance. Analysis of variance revealed a significant effect of drought on relative water content, membrane stability index, plant height, and yield traits. The genotypes Pusa1103, Pusa362, and ICC4958 were found most promising genotypes for drought tolerance as they maintained the higher value of osmotic regulations and yield characters. The results were further supported by a sequence similarity approach for the dehydrin gene when analyzed for the presence of single nucleotide polymorphisms (SNPs) and indels. Homozygous indels and single nucleotide polymorphisms were found after the sequencing in some of the selected genotypes.

scholarly journals Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands

2020 ◽  
Vol 8 (11) ◽  
pp. 1755
Author(s):  
Evert Drijver ◽  
Joep Stohr ◽  
Jaco Verweij ◽  
Carlo Verhulst ◽  
Francisca Velkers ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Pan Genome ◽  
Next Generation Sequencing Analysis ◽  
Long Read ◽  
Short Read Sequence ◽  
High Degree

Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1–pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1–pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNPs) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences, and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1–pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1–pST12 plasmids revealed a low number of SNP differences (range of 0–9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. Next generation sequencing analysis of blaCMY-2-containing IncI1–pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.

Description of Sulfitobacter sediminilitoris sp. nov., isolated from a tidal flat

2020 ◽  
Vol 367 (9) ◽  
Author(s):  
Sooyeon Park ◽  
Siyu Chen ◽  
Jung-Sook Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Type Strains

ABSTRACT A Gram-stain-negative bacterial strain, JBTF-M27T, was isolated from a tidal flat from Yellow Sea, Republic of Korea. Neighbor-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M27T fell within the clade comprising the type strains of Sulfitobacter species. Strain JBTF-M27T exhibited the highest 16S rRNA gene sequence similarity (98.8%) to the type strain of S. porphyrae. Genomic ANI and dDDH values of strain JBTF-M27T between the type strains of Sulfitobacter species were less than 76.1 and 19.2%, respectively. Mean DNA-DNA relatedness value between strain JBTF-M27T and the type strain of S. porphyrae was 21%. DNA G + C content of strain JBTF-M27T from genome sequence was 57.8% (genomic analysis). Strain JBTF-M27T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid. The major polar lipids of strain JBTF-M27T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M27T is separated from recognized Sulfitobacter species. On the basis of the data presented, strain JBTF-M27T ( = KACC 21648T = NBRC 114356T) is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter sediminilitoris sp. nov. is proposed.

scholarly journals Genomic Analysis of an Attenuated Chlamydia abortus Live Vaccine Strain Reveals Defects in Central Metabolism and Surface Proteins

2009 ◽  
Vol 77 (9) ◽  
pp. 4161-4167 ◽  
Author(s):  
L. S. Burall ◽  
A. Rodolakis ◽  
A. Rekiki ◽  
G. S. A. Myers ◽  
P. M. Bavoil
Keyword(s):  
Pyruvate Kinase ◽  
Vaccine Strain ◽  
Genomic Analysis ◽  
Live Vaccine ◽  
Surface Proteins ◽  
Comparative Genomic ◽  
Temperature Sensitive ◽  
Nucleotide Polymorphisms ◽  
Chlamydia Abortus ◽  
Virulence Attenuation

ABSTRACT Comparative genomic analysis of a wild-type strain of the ovine pathogen Chlamydia abortus and its nitrosoguanidine-induced, temperature-sensitive, virulence-attenuated live vaccine derivative identified 22 single nucleotide polymorphisms unique to the mutant, including nine nonsynonymous mutations, one leading to a truncation of pmpG, which encodes a polymorphic membrane protein, and two intergenic mutations potentially affecting promoter sequences. Other nonsynonymous mutations mapped to a pmpG pseudogene and to predicted coding sequences encoding a putative lipoprotein, a sigma-54-dependent response regulator, a PhoH-like protein, a putative export protein, two tRNA synthetases, and a putative serine hydroxymethyltransferase. One of the intergenic mutations putatively affects transcription of two divergent genes encoding pyruvate kinase and a putative SOS response nuclease, respectively. These observations suggest that the temperature-sensitive phenotype and associated virulence attenuation of the vaccine strain result from disrupted metabolic activity due to altered pyruvate kinase expression and/or alteration in the function of one or more membrane proteins, most notably PmpG and a putative lipoprotein.

scholarly journals Chromosome 1 Sequence Analysis of C57BL/6J-Chr1KM Mouse Strain

2017 ◽  
Vol 2017 ◽  
pp. 1-9
Author(s):  
Fuyi Xu ◽  
Tianzhu Chao ◽  
Yiyin Zhang ◽  
Shixian Hu ◽  
Yuxun Zhou ◽  
...  
Keyword(s):  
Mouse Strain ◽  
Sequence Similarity ◽  
Chromosome 1 ◽  
Nucleotide Polymorphisms ◽  
Mus Musculus Domesticus ◽  
Entire Genome ◽  
Functional Variants ◽  
Outbred Mouse ◽  
Km Mouse ◽  
New Perspective

The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms (SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. Moreover, 46,590 of them were classified as novel mutations. Further functional annotation identified 155 genes harboring potentially functional variants, among which 27 genes have been associated with human diseases. We then performed sequence similarity and Bayesian concordance analysis using the SNPs identified on Chr 1 and their counterparts in three subspecies, Mus musculus domesticus, M. m. musculus, and M. m. castaneus. Both analyses suggested that the Chr 1 sequence of B6-Chr1KM was predominantly derived from M. m. domesticus while 9.7% of the sequence was found to be from M. m. musculus. In conclusion, our analysis provided a detailed description of the genetic variations on Chr 1 of B6-Chr1KM and a new perspective on the subspecies origin of KM mouse which can be used to guide further genetic studies with this mouse strain.

scholarly journals Searching for a “Hidden” Prophage in a Marine Bacterium

2009 ◽  
Vol 76 (2) ◽  
pp. 589-595 ◽  
Author(s):  
Yanlin Zhao ◽  
Kui Wang ◽  
Hans-Wolfgang Ackermann ◽  
Rolf U. Halden ◽  
Nianzhi Jiao ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Genomic Analysis ◽  
Bioinformatic Analysis ◽  
Open Reading Frames ◽  
Careful Examination ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Genomic Analyses ◽  
Experimental Laboratory ◽  
Bacterial Genes

ABSTRACT Prophages are common in many bacterial genomes. Distinguishing putatively viable prophages from nonviable sequences can be a challenge, since some prophages are remnants of once-functional prophages that have been rendered inactive by mutational changes. In some cases, a putative prophage may be missed due to the lack of recognizable prophage loci. The genome of a marine roseobacter, Roseovarius nubinhibens ISM (hereinafter referred to as ISM), was recently sequenced and was reported to contain no intact prophage based on customary bioinformatic analysis. However, prophage induction experiments performed with this organism led to a different conclusion. In the laboratory, virus-like particles in the ISM culture increased more than 3 orders of magnitude following induction with mitomycin C. After careful examination of the ISM genome sequence, a putative prophage (ISM-pro1) was identified. Although this prophage contains only minimal phage-like genes, we demonstrated that this “hidden” prophage is inducible. Genomic analysis and reannotation showed that most of the ISM-pro1 open reading frames (ORFs) display the highest sequence similarity with Rhodobacterales bacterial genes and some ORFs are only distantly related to genes of other known phages or prophages. Comparative genomic analyses indicated that ISM-pro1-like prophages or prophage remnants are also present in other Rhodobacterales genomes. In addition, the lysis of ISM by this previously unrecognized prophage appeared to increase the production of gene transfer agents (GTAs). Our study suggests that a combination of in silico genomic analyses and experimental laboratory work is needed to fully understand the lysogenic features of a given bacterium.

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